On Thu, Apr 21, 2011 at 5:27 AM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Thu, Apr 21, 2011, vhakkim boy wrote:
>
> > | ERROR: PMEMD does not support intermolecular PRFs!
>
> This is one of those errors that is never supposed to happen(!). There is
> no
> way to debug it without having access to the input that triggered it.
>
Agreed. The problem here is that one of Bob's 'pseudo-residue fragments'
spans across residues that are considered part of 2 molecules (according to
SOLVENT_POINTERS and ATOMS_PER_MOLECULE). It's likely that this happened
because of an "improperly" create topology file. Of course, how exactly he
split the workload in pmemd is not something I put sufficient amount of time
into understanding, so I don't know the machinery behind it.
Specifically what we need here, though, is the details of EXACTLY how you
created your topology file.
All the best,
Jason
> ...dac
>
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Apr 21 2011 - 08:30:04 PDT
